Antibiotic-Induced Perturbations of the Gut Microbiota Alter Ileal MicroRNA Expression Profiles in Non-Obese Diabetic Mice

Background: Disruptions to the intestinal microbiota in early life increase the risk for autoimmune diseases, such as type 1 diabetes (T1D). A single course of antibiotic treatment (1PAT) from 5-10 days of life accelerated T1D development in male non-obese diabetic (NOD) mice, inducing substantial changes in gut microbial composition and ileal gene expression. MicroRNAs (miRNAs) are important post-transcriptional regulators of gene expression, and recent findings suggest an association of particular miRNAs with T1D pathogenesis. Here we investigated the role of ileal miRNAs in microbiota-mediated regulation of host protein-encoding genes.

Methods: We treated NOD mice of 5-10 days of age with 1PAT only or with no antibiotics (Control), and a group of 1PAT-mice were given cecal microbiota from healthy donors, as a restorative (Restore). Ileal mRNA and miRNA gene expression were evaluated by RNA-Seq and NanoString, respectively, with further quantitation using RT- qPCR. We then employed a computational approach to predict the interactions between differentially expressed mRNAs and miRNAs.

Results: Receiving cecal microbiota transfer rescued the antibiotic-induced acceleration of T1D in NOD mice. Unsupervised hierarchical clustering of mRNA and miRNA expression showed restorative effects of the cecal microbiota transfer at a global level. Among 599 miRNAs measured, 68 had significantly differential expression between treatment groups, including six major miRNAs that responded to both antibiotic exposure and microbiota restoration. These six miRNAs were predicted to target 432 significantly differential mRNAs, many related to host defenses and inflammation. Particular miRNAs also were identified to regulate critical antimicrobial genes via multiple signaling
pathways.

Conclusion: These findings provide evidence that perturbations of the gut microbiota alter ileal miRNA expression profiles which further impact mRNA gene expression. Signaling from both the 1PAT-perturbed and the cecally transplanted restored microbiota involve specific miRNA expression differences to affect ileal mRNA expression. Further investigations of the identified miRNAs and their targeted mRNA genes will deepen insights into the role of miRNAs in mediating microbiota-host interactions and T1D development.